def test_hmmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('20aa-alitest.fa', td) as prot, \
TestData('20aa.hmm', td) as hmm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2,3,4,5):
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task_single = tasks.get_hmmscan_task(prot, out_single,
hmm, 1.0, 1,
self.hmmscan_cfg)
aln_task_multi = tasks.get_hmmscan_task(prot, out_multi,
hmm, 1.0, n_threads,
self.hmmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
print(os.listdir(td), file=sys.stderr)
print(open(out_single).read())
alns_single = pd.concat(hmmscan_to_df_iter(out_single))
alns_multi = pd.concat(hmmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['domain_i_evalue'].sort_values() == \
alns_multi['domain_i_evalue'].sort_values()))
def test_hmmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('20aa-alitest.fa', td) as prot, \
TestData('20aa.hmm', td) as hmm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2, 3, 4, 5):
db_task = tasks.get_hmmpress_task(
hmm, self.hmmpress_cfg)
aln_task_single = tasks.get_hmmscan_task(
prot, out_single, hmm, 1.0, 1, self.hmmscan_cfg)
aln_task_multi = tasks.get_hmmscan_task(
prot, out_multi, hmm, 1.0, n_threads,
self.hmmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
print(os.listdir(td), file=sys.stderr)
print(open(out_single).read())
alns_single = pd.concat(hmmscan_to_df_iter(out_single))
alns_multi = pd.concat(hmmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['domain_i_evalue'].sort_values() == \
alns_multi['domain_i_evalue'].sort_values()))
def test_hmmpress_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-profile.hmm', td) as tf:
task = tasks.get_hmmpress_task(tf, self.hmmpress_cfg)
run_tasks([task], ['run'])
status = check_status(task)
print(os.listdir(td), file=sys.stderr)
for ext in self.extensions:
self.assertTrue(os.path.isfile(tf + ext))
self.assertEquals(status.status, 'up-to-date')
def test_hmmpress_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-profile.hmm', td) as tf:
task = tasks.get_hmmpress_task(tf, self.hmmpress_cfg)
run_tasks([task], ['run'])
status = check_status(task)
print(os.listdir(td), file=sys.stderr)
for ext in self.extensions:
self.assertTrue(os.path.isfile(tf + ext))
self.assertEquals(status.status, 'up-to-date')
def test_hmmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-profile.hmm', td) as hmm, \
TemporaryFile(td) as out:
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task = tasks.get_hmmscan_task(prot, out, hmm, 1.0, 1,
self.hmmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = open(out).read()
print(aln)
self.assertEquals(aln.count('accession'), 2)
self.assertIn('i-Evalue', aln)
def test_hmmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-profile.hmm', td) as hmm, \
TemporaryFile(td) as out:
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task = tasks.get_hmmscan_task(prot, out, hmm, 1.0, 1,
self.hmmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = open(out).read()
print(aln)
self.assertEquals(aln.count('accession'), 2)
self.assertIn('i-Evalue', aln)